Self-incompatibility Alleles Research Articles

Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes

Rahemi, A., Gradziel T.M., Chaparro J.X., Folta, K.M., Taghavi, T., Fatahi, R., Ebadi, A. and Hassani, D. 2015. Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145-1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD+EM-Pc1ConsRD and EM-Pc2ConsFD+EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%...

Identification of the Er1 resistence gene and RNase S-alleles in Malus prunifolia var. ringo rootstock

Woolly apple aphid (WAA; Eriosoma lanigerum Hausm.) is a major insect pest that has significant economic impact on apple growers worldwide. Modern breeding technologies rely on several molecular tools to help breeders select genetic determinants for traits of interest. Consequently, there is a need for specific markers linked to the genes of interest. Apple scions and rootstocks have an additional barrier to the introduction of pest resistance genes due to the presence of self-incompatibility S-RNase alleles. The genetic characterization and early identification of these alleles can amplify the contribution of a breeding program to the selection of resistant genitors that are as compatible as possible. In this study, we identified the Er1 gene involved in the resistance to WAA in Malus prunifolia var. ringo, also known as ‘Maruba Kaido’ rootstock, and we analyzed the inheritance pattern of the WAA resistance Er1 gene in a segregant population derived from Malus pumila ‘M.9’ and ‘Maruba Kaido’ rootstocks. The self-incompatibility of S-RNase alleles S6S26 of ‘Maruba Kaido’ were also identified along with their inheritance pattern. We also confirmed the identification of the S1S3 alleles in the ‘M.9’ rootstock. To the best of our knowledge, this is the first study to characterize WAA resistance and RNase S-alleles in ‘Maruba Kaido’. Furthermore, we discuss the potential use of the genetic markers for these genes and their potential impact on apple breeding programs.

Allele-specific PCR detection of sweet cherry self-incompatibility alleles S<sub>3</sub>, S<sub>4</sub> and S<sub>9</sub> using consensus and allele-specific primers in the Czech Republic

  Prunus avium species of the Rosaceae family exhibit gametophytic self-incompatibility. Determination of the self-incompatibility genotype of individuals is essential for genetic studies and the development of informed management strategies. The PCR-based detection of S-allele helps to promote and speed up traditional breeding activity and hence molecular analysis of the perspective genotypes has become more intensive in all cherry growing countries. The alleles S<sub>3</sub>, S<sub>4</sub> and S<sub>9</sub> from 34 accessions of Czech collections were determined using the polymerase chain reaction (PCR) method. Initially, DNA extracts were amplified with consensus primers that amplify across the first, second, or both introns of the S-ribonuclease gene which shows a considerable length polymorphism. The new allele specific primers were designed with the goal to overcome some occurring difficulties in the detection of expected alleles by previously published allele specific primers. S-alleles fragments of standard cultivars used in this study were PCR amplified, sequenced to validate the designed primers. The study demonstrates the advantage of newly designed primers application in testing of sweet cherry genotypes.    

Initial invasion of gametophytic self-incompatibility alleles in the absence of tight linkage between pollen and pistil S alleles.

In homomorphic self-incompatibility (SI) systems of plants, the loci controlling the pollen and pistil types are tightly linked, and this prevents the generation of compatible combinations of alleles expressing pollen and pistil types, which would result in self-fertilization. We modeled the initial invasion of the first pollen and pistil alleles in gametophytic SI to determine whether these alleles can stably coexist in a population without tight linkage. We assume pollen and pistil loci each carry an incompatibility allele S and an allele without an incompatibility function N. We assume that pollen with an S allele are incompatible with pistils carrying S alleles, whereas other crosses are compatible. Ovules in pistils carrying an S allele suffer viability costs because recognition consumes resources. We found that the cost of carrying a pistil S allele allows pollen and pistil S alleles to coexist in a stable equilibrium if linkage is partial. This occurs because parents that carry pistil S alleles but are homozygous for pollen N alleles cannot avoid self-fertilization; however, they suffer viability costs. Hence, pollen N alleles are selected again. When pollen and pistil S alleles can coexist in a polymorphic equilibrium, selection will favor tighter linkage.

DETECTION OF PEAR S-ALLELES BY SETTING UP A REVISED IDENTIFICATION SYSTEM

Pear (Pyrus communis L.) cultivars are self-incompatible and their adequate fruit set depends on the presence of pollinizer trees with compatibility of bloom period and alleles. This research was carried out in order to identify the self-incompatibility alleles in pear cultivars of the Iranian National Pear Collection. Partial or complete sequences of more than 200 pear S-alleles have been obtained from NCBI and aligned by ClustalW2 in order to compare their conserved regions for categorization of the sequences and subsequent primer design. All deposited S-alleles were separated based on the original species and sequence in 63 divergent sequences, and C2 and C3 conserved regions were used for FB-F/FB-R2 non-specific primer designing. Following PCR amplification of S-alleles, DraI, EcoRI, MspI and HaeIII restriction maps of amplified regions were compared to expected maps from previously identified S-alleles. The results showed homonym groups of alleles, also synonymous alleles such as S22 and S3 in the data bank. Detection of S-alleles in pear cultivars demonstrated 21, 10.5, 13.1 and 7.8% of frequencies, respectively for S1, S2, S4 and S5 alleles. Interestingly, the S42 rare allele from P. ussuriensis was detected in cultivar 'Konjuni' originating from central areas of Iran.

Identification of new S-RNase self-incompatibility alleles and characterization of natural mutations in Iranian almond cultivars

The two main objectives of this research were to identify new S-RNase alleles in Iranian almond cultivars and to characterize naturally occurring mutations in these alleles that may cause self-compatibility. We investigated S genotypes of 22 Iranian almond cultivars using stylar RNase electrophoresis, PCR and DNA sequencing. We report six previously unidentified P. dulcisS-RNase alleles (S45, S46, S47, S48, S49 and S50). Four of 12 tested S-RNases were found to be non-functional in vitro: S49, S50, S24/Sna and S25/S47. Detected point mutations in the C3 coding region of S49- and S50-RNase, leading to the replacement of a highly conserved cysteine and histidine residues, are with the highest probability the reason of these S-RNases inactivity. Results also suggested that ten Iranian almond cultivars display unique S genotype. All presented data confirm Iranian cultivars as valuable almond sources which are of interest to almond breeding and conservation programs.

TRANSITIONS FROM REPRODUCTIVE SYSTEMS GOVERNED BY TWO SELF-INCOMPATIBLE LOCI TO ONE IN FUNGI

Self-incompatibility (SI), a reproductive system broadly present in plants, chordates, fungi, and protists, might be controlled by one or several multiallelic loci. How a transition in the number of SI loci can occur and the consequences of such events for the population's genetics and dynamics have not been studied theoretically. Here, we provide analytical descriptions of two transition mechanisms: linkage of the two SI loci (scenario 1) and the loss of function of one incompatibility gene within a mating type of a population with two SI loci (scenario 2). We show that invasion of populations by the new mating type form depends on whether the fitness of the new type is lowered, and on the allelic diversity of the SI loci and the recombination between the two SI loci in the starting population. Moreover, under scenario 1, it also depends on the frequency of the SI alleles that became linked. We demonstrate that, following invasion, complete transitions in the reproductive system occurs under scenario 2 and is predicted only for small populations under scenario 1. Interestingly, such events are associated with a drastic reduction in mating type number.

Self-incompatibility alleles in Esatern European and Asian almond (Prunus dulcis) genotypes: a preliminary study

Almond [Prunus dulcis (Mill.) D. A. Webb.] as one of the oldest domesticated plants is thought to have originated in central Asia. Gametophytic self-incompatibility of almond is controlled by the highly polymorphic S-locus. The S-locus encodes for an S-ribonuclease (S-RNase) protein in the pistils, which degrades RNA in self-pollen tubes and hence stops their growing. This study was carried out to detect S-RNase allelic variants in Hungarian and Eastern European almond cultivars and Turkish wild growing seedlings, and characterize their S-allele pool. Five new alleles were identifi ed, S31H, S36-S39 in Eastern European local cultivars. The village Bademli and Akdamar island are two distinct places of almond natural occurrence in Turkey. Trees growing wild around Bademli city showed greater genetic diversity than those originated on Akdamar island. Many of the previously described 45 S-RNase alleles have been also detected in these regions. Homology searches revealed that Turkish almonds carried some P. webbii alleles indicating hybridization between the two cultivars and massive introgression events. Our results supply long-awaited information on almond S-allele diversity from regions between the main cultivation centres and the centre of origin of this species; and are discussed from the aspect of methodological developments and evolution of the cultivated almond.

Improved S-genotyping and new incompatibility groups in Japanese plum

The selection of cross-compatible cultivars is essential to ensure fruit set in self-incompatible species like Japanese plum and thus the S-genotype must be determined in order to establish incompatibility groups. In this study an improved Japanese plum S-genotyping method, based in polymerase chain reaction and capillary electrophoresis detection of intron polymorphisms of S-locus genes, S-RNase and SFB, has been assayed and validated in a wide sample of cultivars. This method allows a more precise determination of amplified fragment sizes and therefore a better differentiation of self-incompatibility alleles. The assayed methodology was proven effective in the detection of 13 different S-alleles of S-RNases and SFBs and was used to S-genotype 105 Japanese plum cultivars, 32 of which are described by first time in this work. Analysed cultivars were assigned into 11 incompatibility groups and two new incompatibility groups (XX and XXI) were identified, increasing to 21 the number of incompatibility groups described in this crop.

Mating system shifts on the trailing edge.

The trailing edges of species ranges are becoming a subject of increasing interest as the environment changes due to global warming. Trailing edge populations are likely to face extinction because of a decline in numbers and an inability to evolve new adaptations with sufficient speed. Discussions of character change in the trailing edge have focused on physiological, exomorphic and phenological traits. The mating pattern within populations has not been part of the discourse, in spite of the fact that the mating pattern may affect the ability of populations to respond to environmental change and to maintain their sizes. In this paper, the case is made that a substantial increase in self-fertilization rates may occur via plastic responses to stress. Small populations on the trailing edge are especially vulnerable to environmental change because of inadequate levels of cross-fertilization. Evidence is presented that a deficiency of cross-seed production is due to inadequate pollinator services and a paucity of self-incompatibility alleles within populations. Evidence also is presented that if plants are self-compatible, self-fertilization may compensate in part for this deficiency through a stress-induced increase in levels of self-compatibility and stress-induced alterations in floral morphology that elevate self-pollination. Whereas increased self-fertility may afford populations the time to adapt to their changing environments, it can be concluded that increased selfing is not a panacea for the ills of environmental change, because it will lead to substantial reductions in genetic diversity, which may render adaptation unlikely.

Differential strengths of selection on S-RNases from Physalis and Solanum(Solanaceae)

BackgroundThe S-RNases of the Solanaceae are highly polymorphic self-incompatibility (S-) alleles subject to strong balancing selection. Relatively recent diversification of S-alleles has occurred in the genus Physalis following a historical restriction of S-allele diversity. In contrast, the genus Solanum did not undergo a restriction of S-locus diversity and its S-alleles are generally much older. Because recovery from reduced S-locus diversity should involve increased selection, we employ a statistical framework to ask whether S-locus selection intensities are higher in Physalis than Solanum. Because different S-RNase lineages diversify in Physalis and Solanum, we also ask whether different sites are under selection in different lineages.ResultsMaximum-likelihood and Bayesian coalescent methods found higher intensities of selection and more sites under significant positive selection in the 48 Physalis S-RNase alleles than the 49 from Solanum. Highest posterior densities of dN/dS (ω) estimates show that the strength of selection is greater for Physalis at 36 codons. A nested maximum likelihood method was more conservative, but still found 16 sites with greater selection in Physalis. Neither method found any codons under significantly greater selection in Solanum. A random effects likelihood method that examines data from both taxa jointly confirmed higher selection intensities in Physalis, but did not find different proportions of sites under selection in the two datasets. The greatest differences in strengths of selection were found in the most variable regions of the S-RNases, as expected if these regions encode self-recognition specificities. Clade-specific likelihood models indicated some codons were under greater selection in background Solanum lineages than in specific lineages of Physalis implying that selection on sites may differ among lineages.ConclusionsLikelihood and Bayesian methods provide a statistical approach to testing differential selection across populations or species. These tests appear robust to the levels of polymorphism found in diverse S-allele collections subject to strong balancing selection. As predicted, the intensity of selection at the S-locus was higher in the taxon with more recent S-locus diversification. This is the first confirmation by statistical test of differing selection intensities among self-incompatibility alleles from different populations or species.

GENETIC AND MOLECULAR ANALYSES OF KEY LOCI INVOLVED IN SELF INCOMPATIBILITY AND FLORAL SCENT IN ROSES

Results on our investigations on the genetics and molecular biology of two major characters, self-incompatibility and floral scent will be presented. In crosses between diploid R. multiflora hybrids, the pattern of inheritance of double flowers was often found to be dependent on the direction of the cross. Genetic experiments involving backcrosses of individual progeny to both parents indicated the segregation of self-incompatibility alleles as predicted for a gametophytic SI-system. First data on the genetics and the molecular biology of the S-locus will be presented. The second characteristic, floral scent of roses is very complex due to the large number of secondary metabolites that are involved in rose scent. As this biochemical complexity is very difficult to analyse in tetraploid genomes, we used diploid populations to study the inheritance of individual scent components. Although levels of scent emission were not very high, we were able to characterise several QTLs contributing to the generation of 2-phenyl ethanol, geraniol, nerol, β-citronellol and their acetates. In addition, the position of structural genes for germacren D, alcohol acetyltransferase1, and various O-methyltransferases were mapped on the rose chromosome map. The generation of alcohol-acetates was studied in more detail genetically and on the molecular level.

배추과 작물의 자가불화합성 유전자의 발현 및 조절

In most self-incompatible plant species, recognition of self-pollen is controlled by a single locus, termed the S-locus. The self-incompatibility (SI) system in Brassica is controlled sporophytically by multiple alleles at a single locus, designated as S, and involves cell-cell communication between male and female. Two highly polymorphic S locus genes, SLG (S locus glycoprotein) and SRK (S receptor kinase), have been identified, both of which are expressed predominantly in the stigmatic papillar cell. Gain-of-function experiments have demonstrated that SRK solely determines S haplotype-specificity of the stigma, while SLG enhances the recognition reaction of SI. The sequence analysis of the S locus genomic region of B. campestris (syn. rapa) has led to the identification of an anther-specific gene, designated as SP11/SCR, which is the male S determinant. Molecular analysis has demonstrated that the dominance relationships between S alleles in the stigma were determined by SRK itself, but not by the relative expression level. In contrast, the expression of SP11/SCR from the recessive S allele was specifically suppressed in the S heterozygote, suggesting that the dominance relationships in pollen were determined by the expression level of SP11/SCR. Furthermore, recent studies on recessive allele-specific DNA methylation of Brassica self-incompatibility alleles demonstrate that DNA methylation patterns in plants can vary temporally and spatially in each generation. In this review, we firstly present overview of self incompatibility system in Brassica and then describe dominance relationships in Brassica self- incompatibility regulated by allele-specific DNA methylation.

Population genetics of self-incompatibility and developing self-compatible genotypes in niger (Guizotia abyssinica)

Niger (Guizotia abyssinica (L. f.) Cass. (Asteraceae) is a strictly self-incompatible crop species with a sporophytic self-incompatibility mechanism. This characteristic presents a number of difficulties in plant improvement programs. The objective of this study was to determine the number and distribution of S-alleles in Ethiopian niger populations and to identify and develop self-compatible genotypes with various associated advantages. Several aspects of self-incompatibility in niger were compared in self- and cross-pollination experiments in which seed-set was considered to be a measure of compatibility. Our results indicate the presence of a minimum of ten self-incompatibility alleles and one self-compatibility allele at the S-locus in niger. Most of these alleles behave differently in the pollen and pistil. About two-thirds of the allelic interactions in both the pollen and pistil were dominant/recessive, and one-third were codominant. The reciprocal cross-pollinations (RCPs) resulted in progeny with similar levels of compatibility within and among populations because of a wide distribution of S-alleles in the populations and, consequently, low population differentiation at the S-locus. An analysis of molecular variance (AMOVA) revealed that only 2% of the total genetic variation at the S-locus differentiates the populations. In conclusion, self-compatible genotypes from the Ethiopian niger gene pool have been identified and developed for the first time.

Genetic map-based location of the red clover (Trifolium pratense L.) gametophytic self-incompatibility locus

Red clover is a hermaphroditic allogamous diploid (2n = 2x = 14) with a homomorphic gametophytic self-incompatibility (GSI) system (Trifolium pratense L.). Red clover GSI has long been studied, and it is thought that the genetic control of GSI constitutes a single locus. Although GSI genes have been identified in other species, the genomic location of the red clover GSI-locus remains unknown. The objective of this study was to use a mapping-based approach to identify simple sequence repeats (SSR) that were closely linked to the GSI-locus. Previously published SSR markers were used in this effort (Sato et al. in DNA Res 12:301-364, 2005). A bi-parental cross was initiated in which the parents were known to have one self-incompatibility allele (S-allele) in common. S-allele genotypes of 100 progeny were determined through test crosses and pollen compatibility. Pseudo F(1) linkage analysis isolated the GSI-locus on red clover linkage-group one within 2.5 cM of markers RCS5615, RCS0810, and RCS3161. A second 256 progeny mapping testcross population of a heterozygous self-compatible mutant revealed that this specific self-compatible mutant mapped to the same location as the GSI-locus. Finally, 82 genotypes were identified whose parents putatively shared one S-allele in common from maternal halfsib families derived from two random mating populations in which paternal identity was determined using molecular markers. Unique S-allele identity in the two random mating populations was tentatively inferred based on haplotypes of two highly allelic linkage-group one SSR (RCS0810 and RCS4956), which were closely linked to each other and the GSI-locus. Paternally derived pollen haplotype linkage analysis of RCS0810 and RCS4956 SSR and the GSI-locus again revealed tight linkage at 2.5 and 4.7 cM between the GSI-locus and RCS0810 and RCS4956, respectively. The map-based location of the GSI-locus in red clover has many immediate applications to red clover plant breeding and could be useful in helping to sequence the GSI-locus.

Low S-allele numbers limit mate availability, reduce seed set and skew fitness in small populations of a self-incompatible plant

1. The role of genetic factors in species decline and extinction is the subject of a long-running controversy, with demographical factors often seen as more important for the immediate persistence of populations and species. One gene system that directly links genetic diversity with reproduction, through its influence on fertilization success, is the self-incompatibility (SI) locus in angiosperm plants. Despite the potential importance of SI allele diversity for demographical function, there are few direct measures of S-allele numbers in multiple populations, and no studies have simultaneously measured reproductive output, mate availability, S-allele diversity and pollinator service. 2. We used diallel crosses to estimate S-allele number and mate availability in seven populations of the forb Rutidosis leptorrhynchoides ranging in size from 5 to 100 000 plants. Seed set and correlated paternity were assessed from open-pollinated inflorescences to examine reproductive output and variance in female and male fitness. To assess whether populations were receiving adequate pollinator service, the amount of pollen deposited on open-pollinated stigmas was quantified. 3. We found that small populations (<100 plants) of R. leptorrhynchoides have low S-allele diversity and mate availability and exhibit significant reductions in seed set relative to large populations (>1000 plants) with higher numbers of S-alleles, despite the maintenance of pollinator service. Greater variance in seed set among plants and higher correlated paternity in small populations suggest that low S-allele numbers are directly limiting mate availability and causing the observed reproductive failure. 4. Synthesis and applications. Our work demonstrates that the loss of genetic diversity at the SI locus can have immediate detrimental effects on reproductive performance, despite the maintenance of pollinator service. These results highlight the importance of genetic factors in determining demographical outcomes when clear links between genotype and individual fitness exist, even when populations are not ecologically constrained. This result is important for the conservation and management of many plant species as approximately half of all angiosperm families contain species with genetically controlled SI and the loss of genetic diversity through habitat loss and fragmentation is an ever-increasing reality for plant species worldwide.

GENOTYPING KOREAN APPLE CULTIVARS FOR SELF-INCOMPATIBILITY USING PCR AND CROSS-POLLINATION

Growers of Korean apple cultivars have known that fruit bearing requires cross-pollination. To determine the cross-compatibility of cultivars, we identified the self-incompatibility alleles using PCR-based markers and cross-pollination tests in the field. S-genotypes were determined as follows: 'Hongro' and 'Saenara' are S 1 S 3 , 'Gamhong' and 'Manbok' are S 1 S 9 , 'Seokwang' is S 3 S 5 , and 'Sunhong', 'Seohong', 'Chukwang' and 'Hwahong' are S 1 S 9 . Our results support the view that apples are fully compatible when both S-alleles differ and semi-compatible when they carry one different and one identical allele.

Self-incompatibility alleles in Polish wild pear (Pyrus pyraster (L.) Burgsd.): a preliminary analysis

Wild pear (Pyrus pyraster, syn. P. communis var. pyraster) is thought to be one of the species that gave rise to all other members of the genus Pyrus, although intraspecific hybridizations with cultivated varieties could cause the disappearance of original species characteristics. S-RNase alleles from 7 different wild pear individuals, collected from various regions of Poland, were cloned on the basis of the PCR method and nucleotide sequence analyses. The hypervariable (HV) region is responsible for allele-specific S-RNase activity in the self-incompatibility mechanism. The high level of polymorphism of its sequences may constitute a source of valuable phylogenetic information. From all individuals, 14 sequences were obtained successfully, and 9 of them were novel alleles. Phylogenetic analysis of these alleles was based on the amino acid sequence interpretation of coding regions and intron nucleotide sequences. The research conducted on a limited pool of available P. pyraster alleles gives only an initial insight into possible S-RNase allele polymorphisms in wild populations. At this stage, the results do not confirm a strong influence of cultivated pear species on the wild pear.

Identification of self-incompatibility alleles in Iranian almond cultivars by PCR using consensus and allele-specific primers

SummaryThe S-genotypes of sixteen Iranian cultivars of almond [Prunus dulcis Miller (D.A. Webb)] were determined using a PCR approach with different sets of consensus and allele-specific primers. Using the primers AS1II and AmyC5R (single PCR), or AS1II, AmyC5R, and CEBASf (multiplex PCR), eight PCR products corresponding to known alleles, as well as four bands not corresponding to previously reported sizes, were amplified. PCR with the second intron primers EM-PC2consFD and EM-PC3consRD, and the first intron primers PaConsI-F and EM-PC1consRD, resulted in the amplification of 12 alleles S1,S2,S3,S7,S8,S9,S10,S12,S13,S23,S27, and S29. A putative new allele was detected in the cultivar ‘Mamaei’, which corresponded to PCR products of 1,780 bp, 1,400 bp, and 370 bp using AS1II and AmyC5R, EM-PC2consFD and EM-PC3consRD, and PaConsI-F and EM-PC1consRD, respectively. Products of 850 bp, 520 bp, and 195 bp, were observed in ‘Shirbadam’ using these primers, indicating another new allele. Some of these results were confirmed using allele-specific primers. The alleles S2,S7, and S13 were most common, as each was found in four of the cultivars assayed. Three new cross-incompatibility groups (CIGs) are proposed on the basis of the genotypes obtained. Employing a combination of consensus and allele-specific primers resulted in complete and more precise genotyping. Identification of S-alleles in all the cultivars assayed, despite their unknown parentages, showed that these PCR techniques provide an efficient and rapid method to genotype almond cultivars.

Genetic characterisation of seed yield and fertility traits in perennial ryegrass (Lolium perenne L.)

Seed yield is a trait of major interest for the key grassland species Lolium perenne L. An F2 mapping population of perennial ryegrass (VrnA), recently characterised for vernalisation response, was assessed in a glasshouse for traits related to seed yield based on a lattice design with four replications over 2 years. The traits heading date, plant height, length of panicles, number of panicles per plant, seed yield per panicle, flag leaf length, flag leaf width and seed yield per plant revealed repeatabilities ranging from 41 to 76% and a considerable amount of genetic variation in the VrnA population. Path analysis partitioned the direct and indirect effects of seed yield components on seed yield per plant. Seed yield per panicle showed the highest effect on total seed yield. The adjusted mean values of each trait and a genetic linkage map consisting of 97 anonymous and 85 gene associated DNA markers were used for quantitative trait loci (QTL) analysis. Of particular interest were two QTL on linkage group (LG) 1 and LG 2, explaining 41 and 18%, respectively, of the observed phenotypic variation for the trait seed yield per panicle. Both QTL co-located with two major QTL for total seed yield per plant possibly representing the S and Z loci of the gametophytic self incompatibility (SI) system of perennial ryegrass. The diversity of SI alleles in mapping parents and the degree of heterozygosity at SI loci in the full sib progeny determines the interference of self incompatibility with seed production.